The Defendant has three parts in its Motion One Dealing with the Claims 1-V, another dealing with the Affirmative Defense and another Counter Claims, can I strike or answer each one as separately through 3 motions?
A motion is another name for asking the court for something. Here, you wouldn't be filing a "motion", but merely responding to the defendant's counterclaims. The legal term for that is a reply.
As for the rest of Defendant's responsive pleading, there is no need to "answer" the answer. The defendant is merely responding to the claims factually while denying them, then stating what he expects his affirmative defenses to be. After you file your reply to the counterclaims, the next thing to happen is a trial; meaning, the plaintiff is put to his burden of proof on his complaint and the defendant on his counterclaims (although the court will probably set a pre-trial to discuss the possibility of settlement).
Not enough information in the post to give you a full answer. I will tell you that if there is a counter claim you need to file an answer of your own with the appropriate affirmative defenses.